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Masterfile.pir
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Masterfile.pir
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#
# Masterfile : a container for a parsed masterfile
#
- PerlClass PirObject::Masterfile
- InheritsFrom PirObject
- FieldsTable
# Field name Struct Type Comments
#---------------------- ------- ------------------- -----------------------
filename single string Filename of masterfile
header array string Multiline comment at top of masterfile. If already there, they must be removed
comment array string Multiline comment at top of masterfile. If already there, they must be kept.
contigs array <MasterfileContig> Contig sequences and annots
- EndFieldsTable
- Methods
our $RCS_VERSION='$Id: Masterfile.pir,v 1.40 2012/01/21 20:53:09 nbeck Exp $';
our ($VERSION) = ($RCS_VERSION =~ m#,v ([\w\.]+)#);
# Reads a masterfile from a file and populates a PirObject::Masterfile structure with it.
sub ObjectFromMasterfile { # yamp, yet another masterfile parser, and an ugly one too.
my $self = shift;
my $filename = shift;
my $RemoveIupac = shift || 0;
my $fh = new IO::File "<$filename"
or die "Can't read from '$filename': $!\n";
my @lines = <$fh>; # slurp it all in!
$fh->close();
chomp @lines;
my $mf = $self->new( filename => $filename );
my $row = 0;
my $header = [];
my $comment_header = [];
my $after_header = 0;
while ($row < @lines && $lines[$row] !~ m#^>#) {
if ($lines[$row] =~ m#^;;\s*end mfannot#) {
$row++;
$after_header = 1;
next;
}
push(@$header,$lines[$row++]) if $after_header == 0;
push(@$comment_header,$lines[$row++]) if $after_header == 1;
}
$mf->set_header($header);
my $scalar = scalar(@$header);
my $MFheaderisDef = scalar(@$comment_header);
$MFheaderisDef == 0 ? $mf->set_comment($header) : $mf->set_comment($comment_header) ;
my $contigs = [];
# This loops parses each contig.
for (;;) {
last if $row >= @lines;
my $contig = PirObject::MasterfileContig->new();
my ($faname,$namecomments) = ($lines[$row++] =~ m#^>\s*(\S+)(.*)#)
or die "Can't parse header line of masterfile '$filename'. Line is:\n" . $lines[$row];
$namecomments =~ s/\s*$//;
$contig->set_name($faname);
$contig->set_geneticcode($1) if $namecomments ne "" && $namecomments =~ m/\/trans\s*=\s*(\d+)/i;
$contig->set_namecomments($namecomments) if $namecomments ne "";
my $seq = "";
my %annotexp = (); # expected
my $allannots = [];
my $seqpos = 0; # in computer coordinates, not biological coordinates!
my $linenumber = 0; # arbitrary counter
while ($row < @lines) {
$linenumber++;
my $line = $lines[$row++];
next if $line =~ m#^\s*$#; # ignore blank lines
$row--, last if $line =~ m#^>#; # That means 'next contig'!
if ($line =~ m#^\s*\d*\s*([^;].*)#) {
my $dna = $1;
next if $dna =~ m/^\s+$/;
$dna =~ tr/ \r\n\t//d;
if ($RemoveIupac == 0) {
die "Bad characters in sequence line?!??\nLine: $line\n"
unless $dna =~ m#^[acgtnN!]+$#;
$seq .= $dna; # includes special characters such as '!'
$seqpos += ($dna =~ tr/acgtACGTnN/acgtACGTnN/) ; # count without the '!'s.
}
else {
die "Bad characters in sequence line?!??\nLine: $line\n"
unless $dna =~ m#^[uUyrwskmbdhvxUYRWSKMBDHVXACGTacgtnN!]+$#;
$seq .= $dna; # includes special characters such as '!'
$seqpos += ($dna =~ tr/uUyrwskmbdhvxUYRWSKMBDHVXacgtACGTnN/uUyrwskmbdhvxUYRWSKMBDHVXacgtACGTnN/);# count without the '!'s.
$seq =~ tr/uUyrwskmbdhvxUYRWSKMBDHVX/TTNNNNNNNNNNNNNNNNNNNNNN/;
}
next;
}
if ($line =~ m#^;\s*([G])-(\S+)\s+(<==\*?|\*?==>)\s+(start|end|point)(.*)#) {
my ($type,$name,$arrow,$startend,$comment) = ($1,$2,$3,$4,$5);
my $intron_type = "";
$intron_type = $1 if $line =~ m#/group=(\S+)#;
my $multicomment = [];
for (;$row < @lines;$row++) {
last unless $lines[$row] =~ m#^;# && $lines[$row-1] =~ m#\\\s*$#;
push(@$multicomment,$lines[$row]);
}
my $pos = $arrow =~ />/ ?
($startend eq "start" || $startend eq "point" ? $seqpos+1 : $seqpos)
: ($startend eq "end" ? $seqpos+1 : $seqpos);
my $annotkey = lc "$type-$name";
### structure of date : a hash called annotexp, contains a
### table. This on contains an other hash for storing annotation
### The last hash array has 3 keys :
### 1 -> start : if it's defined, start pos is defined in annotation
### 2 -> end : if it's defined, end pos is defined in annotation
### 3 -> annot : contains the annotation itself
if ($startend eq "point") {
my $annot = new PirObject::AnnotPair( type => $type,
introntype => $intron_type,
genename => $name,
direction => $arrow,
);
$annot->SetMultipleFields(
startpos => $pos,
endpos => $pos,
startline => $line,
startmulticomment => $multicomment,
startlinenumber => $linenumber,
);
push(@$allannots,$annot);
}
else {
if (defined $annotexp{$annotkey}){
my $table = $annotexp{$annotkey};
if ($startend eq "start"){
my $count=0;
my $hasdefined = 0; # a variable that allows to
START : while ($count < scalar(@$table)){ # goo over the table containing annotation
my $infos = $table->[$count];
my $state = $infos->{'startend'}; # here we get if it's start or stop
if ($state eq 'start' or $state eq 'finish') { # It mean start is already defined
$count++;
next START;
}
else { # Means that end
my $annot = $infos->{'annotation'};
$annot->SetMultipleFields(
startpos => $pos,
startline => $line,
startmulticomment => $multicomment,
startlinenumber => $linenumber,
);
push(@$allannots,$annot);
$infos->{'startend'} = 'finish';
$hasdefined = 1;
last START;
}
}
if ($hasdefined == 0) { # it means that annotation array has been running without finding an empty
#case, a corresponding annotation in existing annotation
my $newinfos = {};
$newinfos->{'startend'} = 'start'; # It's just to define the thing
my $annot = new PirObject::AnnotPair(
type => $type,
introntype => $intron_type,
genename => $name,
direction => $arrow,
);
$annot->SetMultipleFields(
startpos => $pos,
startline => $line,
startmulticomment => $multicomment,
startlinenumber => $linenumber,
);
$newinfos->{'annotation'} = $annot;
push (@$table, $newinfos);
}
} # End of case if it's start
else { # case
my $count=0;
my $hasdefined = 0; # a variable that allows to
STOP : while ($count < scalar(@$table)){ # goo over the table containing annotation
my $infos = $table->[$count];
my $state = $infos->{'startend'}; # here we get if it's start or stop
if ($state eq 'end' or $state eq 'finish' ) { # It mean start is already defined
$count++;
next STOP;
}
else { # Means that end
my $annot = $infos->{'annotation'};
$annot->SetMultipleFields(
endpos => $pos,
endline => $line,
endmulticomment => $multicomment,
endlinenumber => $linenumber,
);
push(@$allannots,$annot);
$infos->{'startend'} = 'finish';
$hasdefined = 1;
last STOP;
}
}
if ($hasdefined == 0) { # it means that annotation array has been running without finding an empty
#case, a corresponding annotation in existing annotation
my $newinfos = {};
$newinfos->{'startend'} = 'end'; # It's just to define the thing
my $annot = new PirObject::AnnotPair(
type => $type,
introntype => $intron_type,
genename => $name,
direction => $arrow,
);
$annot->SetMultipleFields(
endpos => $pos,
endline => $line,
endmulticomment => $multicomment,
endlinenumber => $linenumber,
);
$newinfos->{'annotation'} = $annot;
push (@$table, $newinfos);
}
} # End of case if it's stop
} # End of if it's :
else {
my $annot = new PirObject::AnnotPair(
type => $type,
introntype => $intron_type,
genename => $name,
direction => $arrow,
);
if ($startend eq "start") {
$annot->SetMultipleFields(
startpos => $pos,
startline => $line,
startmulticomment => $multicomment,
startlinenumber => $linenumber,
);
}
elsif ($startend eq "end") { # $startend eq "end"
$annot->SetMultipleFields(
endpos => $pos,
endline => $line,
endmulticomment => $multicomment,
endlinenumber => $linenumber,
);
}
my $infos = {}; # hash array containing, start stop, and the annot
$infos->{'startend'} = $startend; # It's just to define the thing
$infos->{'annotation'} = $annot;
my $table = [];
push (@$table, $infos); # we put the hashing table in the table
$annotexp{$annotkey} = $table;
}
next;
} # End of if line is like that
}
if ($line =~ m#^;#) {
my $multicomment = [];
for (;$row < @lines;$row++) {
last unless $lines[$row] =~ m#^;# && $lines[$row-1] =~ m#\\\s*$#;
push(@$multicomment,$lines[$row]);
}
my $annot = new PirObject::AnnotPair(
type => "C", # a comment
startpos => $seqpos+1,
startline => $line,
startmulticomment => $multicomment,
startlinenumber => $linenumber,
);
push(@$allannots,$annot);
next;
}
die "Unexpected line:\n$line\n";
} # loop through lines of contig
# checking annotations
foreach my $annot (@$allannots) {
if ($annot->type eq 'G') {
# For the genename, deleting the _X : the number of each copy
my $newgename = $annot->genename;
$newgename =~ s/\_\d+//;
if ($newgename =~ m#-I\d+-(\S+)$#) { # special case for G-cox1_2-I3-orf232
$newgename = $1;
}
$annot->set_genename($newgename);
# If it's a gene
if ($annot->genename =~ /Sig-(.+)$/){
$annot->set_genename ($1);
$annot->set_type("S")
}
elsif ($annot->genename =~ /-E\d+$/ || $annot->genename =~ /-E\d+-\S+$/) { # If it's an exon
my @genenamecut = split ("-", $annot->genename); # Split the name by -
$annot->set_genename ($genenamecut[0]) if $genenamecut[0] ne ""; # Give only the genename to the exon
$annot->set_type("E"); # Se t a new type
}
elsif ($annot->genename =~ /-I\d+$/ || $annot->genename =~ /-I\d+-\S+$/) { # If it's an exon
my @genenamecut = split ("-", $annot->genename); # Split the name by -
$annot->set_genename ($genenamecut[0]) if $genenamecut[0] ne ""; # Give only the genename to the exon
$annot->set_type("I"); # Se t a new type
}
elsif ($annot->genename =~ /(trn[\w|?]*)\([\w|?]*\)/) { # It's a tRNA
my $newtrnaname = $1; # Just take trnA.... as gene name
$annot->set_genename ($newtrnaname);
}
}
}
undef %annotexp;
$contig->set_sequence($seq);
$contig->set_annotations($allannots);
my $seqlen = ($seq =~ tr/ACGTNacgtn/ACGTNacgtn/); # count them
$contig->set_sequencelength($seqlen);
push(@$contigs,$contig);
} # loop through contigs
$mf->set_contigs($contigs);
$mf;
}
sub ObjectToMasterfile {
my $self = shift;
my $filename = shift;
# Print masterfile header
my $fh = new IO::File ">$filename"
or die "Can't write to '$filename': $!\n";
my $header = $self->get_header() || [];
pop(@$header) while @$header && $header->[-1] =~ m#^\s*$#;
if (@$header) {
print $fh join("\n",@$header),"\n";
}
my $contigs = $self->get_contigs() || [];
foreach my $contig (@$contigs) {
my $name = $contig->get_name();
my $namecomments = $contig->get_namecomments() || "";
print $fh "\n\n";
print $fh ">$name$namecomments\n";
my $posannots = [];
my $annots = $contig->get_annotations();
my $fullseq = $contig->get_sequence(); # contains '!'s !
my %start_ac = ();
my %stop_ac = ();
foreach my $annot (@$annots) {
my $type = $annot->type();
next unless $type eq 'AC';
my $start = $annot->startpos();
$start_ac{$start}=1; # biol coordinates
my $stop = $annot->endpos();
$stop_ac{$stop}=1;
}
my $num = 0; # $num will be bio coords
for ( my $i = 0; $i < length($fullseq) ; $i++) {
my $c = substr($fullseq,$i,1);
next if $c eq '!';
$num++; # $num is bio coords
if ( $start_ac{$num} || $stop_ac{$num} ) {
if (substr($fullseq,$i-1,1) ne '!' && $start_ac{$num}) {
substr($fullseq,$i,0) = "!";
$i++;
}
if (substr($fullseq,$i,1) ne '!' && $stop_ac{$num}) {
substr($fullseq,$i+1,0) = "!";
$i++;
}
}
}
ANNOT : foreach my $annot (@$annots) {
my $type = $annot->type() ;
my $start = $annot->startpos();
next if ($type eq "AC" );
my $end = $annot->endpos(); # can be undef
my $arrow = $annot->get_direction() || ">"; # <== or ==> or <==* or *==> or undef
if ($arrow =~ m#>#) {
push(@$posannots, [ $start-1, ($annot->startlinenumber() || 0), "S", $annot]) if defined($start);
push(@$posannots, [ $end, ($annot->endlinenumber() || 0), "E", $annot]) if defined($end);
}
else {
push(@$posannots, [ $start, ($annot->startlinenumber() || 0), "S", $annot]) if defined($start);
push(@$posannots, [ $end-1, ($annot->endlinenumber() || 0), "E", $annot]) if defined($end);
}
}
my $etape = 1;
@$posannots = sort { # Modified by T. HOELLINGER
# Simple case, nucleotide position is different:
return $a->[0] <=> $b->[0] if $a->[0] != $b->[0];
# Simple case, line numbers are available and > 0, so compare them
return $a->[1] <=> $b->[1] if $a->[1] && $b->[1];
# The new sorting function
my $fulllinea = " "; # G-genname ==> start ;; comment
my $fulllineb = " "; # || ||
my $namea = " "; # the genename
my $nameb = " "; # || ||
my $arrowa = " "; # ==> or <==
my $arrowb = " " ; # || ||
my $startorenda = " " ; # as it said start or end
my $startorendb = " " ; # || ||
# Take the line
$fulllinea = $a->[3]->startline if ($a->[2] eq "S");
$fulllinea = $a->[3]->endline if ($a->[2] eq "E");
$fulllineb = $b->[3]->startline if ($b->[2] eq "S");
$fulllineb = $b->[3]->endline if ($b->[2] eq "E");
# Cut the line were there are ;;
my @cutlinea = split (";;", $fulllinea); # do a split
my @cutlineb = split (";;", $fulllineb); # do a split
# Cut the line and identify pattern
my $linea = $cutlinea[0] || ""; # Only take the part before ;;, Delete comments
my $lineb = $cutlineb[0] || ""; # || ||
$linea =~ s/^\s*//; # Delete the spaces before, at the beginning of the description
$lineb =~ s/^\s*//; # || ||
$linea =~ s/\s*$//; # Delete the spaces at the end of the descriptio
$lineb =~ s/\s*$//; # || ||
$linea =~ /([\w|\_\-\d\(\)\?]+)\s*(==>|<==)\s*(start|end)/;
$namea = $1 || ""; # Get the genename
$arrowa = $2 || ""; # Get the arrow
$startorenda = $3 || ""; # Get the start or the end
$lineb =~ /([\w|\_\-\d\(\)\?]+)\s*(==>|<==)\s*(start|end)/;
$nameb = $1 || "";
$arrowb = $2 || "";
$startorendb = $3 || "";
if ($arrowa eq "==>" and $arrowb eq "==>" and $startorenda eq "start" and $startorendb eq "start") {
return $namea cmp $nameb;
}
elsif ($arrowa eq "==>" and $arrowb eq "==>" and $startorenda eq "end" and $startorendb eq "end") {
return $nameb cmp $namea;
}
elsif ($arrowa eq "==>" and $arrowb eq "==>" and $startorenda eq "start" and $startorendb eq "end") {
return $a->[2] cmp $b->[2]; # end before the start
}
elsif ($arrowa eq "==>" and $arrowb eq "==>" and $startorenda eq "end" and $startorendb eq "start") {
return $a->[2] cmp $b->[2]; # end before the start
}
elsif ($arrowa eq "<==" and $arrowb eq "<==" and $startorenda eq "start" and $startorendb eq "start") {
return $nameb cmp $namea;
}
elsif ($arrowa eq "<==" and $arrowb eq "<==" and $startorenda eq "end" and $startorendb eq "end") {
return $namea cmp $nameb;
}
elsif ($arrowa eq "<==" and $arrowb eq "<==" and $startorenda eq "start" and $startorendb eq "end") {
return $b->[2] cmp $a->[2]; # start before the end
}
elsif ($arrowa eq "<==" and $arrowb eq "<==" and $startorenda eq "end" and $startorendb eq "start") {
return $b->[2] cmp $a->[2]; # start before the end
}
else {
return $fulllinea cmp $fulllineb;
}
}@$posannots;
my $seqpos = 0;
my $charpos = 0;
while (@$posannots) {
my $annotinfo = shift(@$posannots);
my ($atpos,$se,$annot) = @$annotinfo[0,2,3];
my $name = $annot->get_genename();
my $block = "";
my $blockpos = $seqpos;
while ($seqpos < $atpos) {
my $char = substr($fullseq,$charpos,1);
my $IsDef = !$char ? 1 : 0;
$block .= $char;
$charpos++;
$seqpos++ if $char ne '!';
}
if (substr($fullseq,$charpos,1) eq "!" && length($block) >= 4 && substr($block,-4,4) =~ m#!#) {
$block .= "!";
$charpos++;
}
if ($block) {
&_FastaBlockToFH($block,$blockpos+1,$fh);
}
my $multicomment = [];
if ($se eq "S") {
print $fh $annot->get_startline(),"\n";
$multicomment = $annot->get_startmulticomment();
}
else { # $se eq "E"
print $fh $annot->get_endline(),"\n";
$multicomment = $annot->get_endmulticomment();
}
if (@$multicomment) {
print $fh join("\n",@$multicomment),"\n";
}
}
my $block = $charpos < length($fullseq) ? substr($fullseq,$charpos) : "";
if ($block) {
&_FastaBlockToFH($block,$seqpos+1,$fh);
}
}
$fh->close();
}
sub _FastaBlockToFH { # not a method
my $seq = shift; # may contain '!' characters!
my $pos = shift;
my $fh = shift;
while ($seq) {
if (length($seq) > 60) {
my $subseq = substr($seq,0,60);
printf $fh "%6d %s\n",$pos,$subseq;
$pos += ($subseq =~ tr/ACGTNacgtn/ACGTNacgtn/); # count them
$seq = substr($seq,60);
next;
}
printf $fh "%6d %s\n",$pos,$seq;
last;
}
}
# Utility routine that precomputes an internal hash the first
# time it's called.
sub GetContigByName {
my $self = shift;
my $contigname = shift;
if (!$self->{'!contigbyname!'}) {
my $cache = $self->{'!contigbyname!'} = {};
my $contigs = $self->get_contigs() || [];
foreach my $contig (@$contigs) {
my $name = $contig->get_name();
next unless defined $name;
$cache->{$name} = $contig;
}
}
$self->{'!contigbyname!'}->{$contigname}; # returns undef if not found.
}
sub SortMasterfile
{
my $self = shift;
my $direction = shift;
my $contigs = $self->contigs;
@$contigs = sort {
my $lenA = length($a->sequence);
my $lenB = length($b->sequence);
if($direction == 1) {
$lenB <=> $lenA;
}
else {
$lenA <=> $lenB;
}
}@$contigs;
}